Contacts of the helix formed by residues 825 - 837 (chain A) in PDB entry 2N8Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A SER 5.6 1.3 - - - +
744A SER* 2.7 31.3 + - - +
746A GLU* 6.5 0.7 - - - -
747A GLN* 5.7 2.5 - - + -
823A THR* 6.5 0.2 - - + -
824A ASP* 1.3 86.7 - - - +
826A ALA* 1.3 65.3 + - - +
827A ASP* 3.7 4.8 + - - +
828A GLN* 3.2 34.7 + - + +
829A VAL* 3.2 6.9 + - - +
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Residues in contact with ALA 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A ASP* 4.4 0.8 + - - -
825A THR* 1.3 73.1 - - - +
827A ASP* 1.3 63.8 + - - +
829A VAL* 3.5 10.2 - - - +
830A MET* 3.2 27.4 + - - +
882A PHE* 5.8 5.1 - - + -
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Residues in contact with ASP 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A SER* 3.4 11.0 - - - -
745A GLN* 2.8 60.3 + - - +
746A GLU* 4.5 13.3 - - - +
825A THR* 3.2 8.7 + - - +
826A ALA* 1.3 79.0 - - - +
828A GLN* 1.3 58.5 + - - +
830A MET* 4.1 2.1 - - - +
831A ALA* 3.0 31.9 + - - +
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Residues in contact with GLN 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A GLY* 3.3 5.2 - - - -
741A SER 3.0 12.5 + - - +
742A SER* 3.0 46.0 + - - +
743A ILE 3.6 23.6 - - - +
744A SER* 4.2 1.6 - - - +
824A ASP* 3.5 19.5 - - - +
825A THR* 3.2 30.6 + - + +
827A ASP* 1.3 82.9 - - - +
829A VAL* 1.3 84.5 + - - +
831A ALA* 4.0 5.1 - - - +
832A SER* 2.7 34.5 + - - +
852A LEU* 4.6 0.2 - - - +
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Residues in contact with VAL 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A GLY* 5.5 2.0 - - - -
824A ASP* 4.8 7.6 - - - +
825A THR 3.2 8.7 + - - +
826A ALA* 3.5 17.3 - - - +
827A ASP 3.3 0.2 - - - -
828A GLN* 1.3 99.1 - - - +
830A MET* 1.3 68.2 + - - +
832A SER* 3.9 4.5 - - - -
833A PHE* 3.1 51.3 + - + -
851A GLU* 6.3 0.2 - - + -
852A LEU* 4.2 14.4 - - + -
860A CYS* 4.0 19.3 - - - -
882A PHE* 4.5 18.4 - - + -
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Residues in contact with MET 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ALA 3.2 14.6 + - - +
827A ASP* 4.1 2.2 - - - +
829A VAL* 1.3 79.1 - - + +
831A ALA* 1.3 67.3 + - - +
832A SER 3.4 0.2 + - - -
833A PHE* 3.4 16.8 + - + +
834A LYS* 3.5 15.4 + - - +
879A TYR* 3.1 42.0 - - + +
880A MET* 5.1 0.9 - - - -
882A PHE* 3.7 23.8 - - + -
883A SER* 3.4 34.8 - - - +
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Residues in contact with ALA 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745A GLN* 5.2 9.9 - - + +
827A ASP* 3.0 25.4 + - - +
828A GLN* 4.0 6.3 - - - +
830A MET* 1.3 81.8 - - - +
832A SER* 1.3 62.0 + - - +
834A LYS* 3.4 14.7 + - - +
835A ILE* 3.5 17.4 - - + +
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Residues in contact with SER 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A GLY* 3.9 14.6 + - - -
742A SER* 4.6 4.7 + - - -
828A GLN* 2.7 25.0 + - - +
829A VAL* 3.9 4.3 - - - -
830A MET 3.3 0.2 - - - -
831A ALA* 1.3 74.7 - - - +
833A PHE* 1.3 65.1 + - - +
835A ILE* 3.0 31.1 + - - +
836A LEU* 3.4 4.5 + - - +
851A GLU* 3.1 29.9 - - - +
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Residues in contact with PHE 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A VAL* 3.1 47.0 + - + -
830A MET* 3.9 12.8 - - + +
831A ALA 3.4 0.4 - - - -
832A SER* 1.3 78.1 - - - +
834A LYS* 1.3 58.6 + - - +
835A ILE 3.1 0.2 + - - -
836A LEU* 3.2 6.1 + - + +
837A ALA* 2.8 31.9 + - - +
843A ILE* 4.2 15.9 - - + -
848A LEU* 3.8 26.2 - - + -
851A GLU* 3.7 18.2 - - + -
852A LEU* 4.6 4.5 - - + -
860A CYS* 4.5 6.7 - - + -
864A MET* 3.6 32.8 - - + -
879A TYR* 3.5 34.5 - - + -
882A PHE* 4.8 2.0 - + - -
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Residues in contact with LYS 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A MET* 3.5 10.8 + - - +
831A ALA* 3.4 11.6 + - - +
832A SER 3.2 0.8 - - - -
833A PHE* 1.3 79.6 - - - +
835A ILE* 1.3 58.6 + - + +
838A GLY* 3.1 25.1 + - - -
879A TYR* 3.5 31.4 - - + +
880A MET* 4.8 20.4 - - - +
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Residues in contact with ILE 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831A ALA* 3.5 19.1 - - + +
832A SER* 3.0 18.3 + - - +
834A LYS* 1.3 81.4 - - + +
836A LEU* 1.3 61.1 + - + +
838A GLY* 3.9 4.9 + - - -
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Residues in contact with LEU 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832A SER 3.4 3.7 + - - +
833A PHE* 3.2 5.1 + - + +
835A ILE* 1.3 82.4 - - + +
837A ALA* 1.3 59.9 + - - +
838A GLY 3.3 2.1 + - - -
839A ASP* 4.4 8.7 + - - +
840A LYS* 4.9 1.7 + - - -
843A ILE* 3.6 26.2 - - + -
847A GLU* 3.6 42.9 - - + +
850A ARG* 4.3 24.0 - - - +
851A GLU* 3.2 42.6 - - + +
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Residues in contact with ALA 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A PHE 2.8 11.4 + - - +
834A LYS 4.0 1.1 - - - -
836A LEU* 1.3 75.8 - - - +
838A GLY* 1.3 52.7 + - - +
839A ASP* 3.0 5.6 - - - +
840A LYS* 2.7 39.6 + - - +
842A TYR 3.5 11.9 - - - +
843A ILE* 3.5 20.0 - - + -
879A TYR* 3.3 31.9 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il